Morgan began his career at Tranmere Rovers, making his debut on 27 August 1996 in a 2–0 victory over Port Vale before spending time on loan at Conference National side Altrincham. The following season, Morgan began to establish himself in the first team at Prenton Park, making 23 appearances in all competitions. Rovers fought their way to the 2000 League Cup Final and with Morgan as an unused substitute, they were defeated 2–1 by Leicester City. However continuing injury problems restricted his first team appearances in the following years and, in 2002, he was allowed to join Doncaster Rovers on a free transfer. He played just three times for Doncaster before being released and instead moved to Morecambe in December 2002. After a spell with Porthmadog, Morgan took over as player-manager of Welsh Premier League side NEWI Cefn Druids, replacing Steve O'Shaughnessy in February 2004. However, he spent just 10 months in the role before stepping down in December 2004 and moving to Rhyl, where he made one appearance before ending his first team playing career at Connah's Quay Nomads.
Managerial career
In 2007, Morgan joined Bangor City as assistant manager to former Tranmere player Neville Powell where they led the side to two consecutive top six finishes and UEFA Cup places.
Aberystwyth Town
Morgan was appointed as manager of his home town team Aberystwyth Town in November 2009, succeeding Brian Coyne. Morgan was joined by his former Tranmere and Wales under-21 teammate Christian Edwards, who had served as caretaker manager of the club during the vacancy, as his assistant manager. In his first season, Morgan took Aberystwyth to a fourth-placed finish. He left the club in February 2012 by mutual consent after a disappointing season.
In November 2012, Morgan was appointed manager of Llandudno. Following his appointment he was named Cymru AllianceManager of the Month. Morgan lead Llandudno to promotion to the Welsh Premier League for the first time in the club's existence after winning the 2014–15 Cymru Alliance. He parted company with the club on 23 October 2017 after five years in charge.
